Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006555.1 Kokia drynarioides strain JFW-HI SEQ_121141, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 979
Length: 1633
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Found at i:699 original size:28 final size:30
Alignment explanation
Indices: 668--725 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
658 TTCATAATTG
*
668 AGTGA-CAAAAAA-TATTTACTAATAGTTA
1 AGTGACCAAAAAAGAATTTACTAATAGTTA
696 AGTGACCAAAAAAGGAATTTACTAATAGTT
1 AGTGACCAAAAAA-GAATTTACTAATAGTT
726 GGGTGACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 7 0.27
31 14 0.54
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (30 bp):
AGTGACCAAAAAAGAATTTACTAATAGTTA
Found at i:1025 original size:9 final size:8
Alignment explanation
Indices: 995--1099 Score: 66
Period size: 9 Copynumber: 11.9 Consensus size: 8
985 ATATTTCTCG
995 TAAAAATAA
1 TAAAAAT-A
1004 TTAAAAATACA
1 -TAAAAAT--A
1015 TAAAAATCA
1 TAAAAAT-A
*
1024 TAAAGATTA
1 TAAA-AATA
1033 TAAAAATA
1 TAAAAATA
1041 TAAAAAATA
1 T-AAAAATA
1050 TAAAAAATA
1 T-AAAAATA
1059 TAAAAATCA
1 TAAAAAT-A
*
1068 GAAAAATTA
1 TAAAAA-TA
* *
1077 TTAAAATT
1 TAAAAATA
*
1085 TTAAAATA
1 TAAAAATA
*
1093 TTAAAAT
1 TAAAAAT
1100 TGTTACATAC
Statistics
Matches: 82, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
8 25 0.30
9 39 0.48
10 17 0.21
11 1 0.01
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (8 bp):
TAAAAATA
Found at i:1052 original size:26 final size:28
Alignment explanation
Indices: 996--1074 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 28
986 TATTTCTCGT
996 AAAAATAATTAAAAATACATAAAAATCATA
1 AAAAAT-A-TAAAAATACATAAAAATCATA
* * *
1026 AAGATTATAAAAATATA-AAAAAT-ATA
1 AAAAATATAAAAATACATAAAAATCATA
*
1052 AAAAATATAAAAAT-CAGAAAAAT
1 AAAAATATAAAAATACATAAAAAT
1075 TATTAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
25 1 0.02
26 21 0.50
27 6 0.14
28 9 0.21
29 1 0.02
30 4 0.10
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.23
Consensus pattern (28 bp):
AAAAATATAAAAATACATAAAAATCATA
Found at i:1146 original size:20 final size:20
Alignment explanation
Indices: 1108--1165 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1098 ATTGTTACAT
1108 ACTTATAAAATAATAAAAAAA
1 ACTTAT-AAATAATAAAAAAA
* *
1129 ACTTATAAATATTTAAAAAA
1 ACTTATAAATAATAAAAAAA
* * *
1149 TCTAATAAATTATAAAA
1 ACTTATAAATAATAAAA
1166 TTAATAAAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 24 0.80
21 6 0.20
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
ACTTATAAATAATAAAAAAA
Found at i:1237 original size:20 final size:21
Alignment explanation
Indices: 1190--1237 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1180 TTAAAATTTT
* *
1190 ATAAAAACCGTATAAAAATTC
1 ATAAAAACCATATAAAAAATC
* *
1211 TTTAAAA-CATATAAAAAATC
1 ATAAAAACCATATAAAAAATC
1231 ATAAAAA
1 ATAAAAA
1238 TTTGAATTGG
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.25
Consensus pattern (21 bp):
ATAAAAACCATATAAAAAATC
Done.